def decorate_interface():
ats = Atoms('interface.xyz')
dataset = spglib.get_symmetry_dataset(ats, symprec=1e-5)
with open('unique_lattice_sites.json', 'w') as f:
json.dump([
list(ats[site_num].position)
for site_num in np.unique(dataset['equivalent_atoms'])
], f)
unique_atoms = []
for at in ats:
unique_atoms.append(at.position)
voronoi = Voronoi(limits=tuple(np.diag(ats.cell)),
periodic=(True, True, False))
cntr = voronoi.compute_voronoi(unique_atoms)
ints_list = []
for site_num in np.unique(dataset['equivalent_atoms']):
for vert in voronoi.get_vertices(site_num, cntr):
ints_list.append(vert.tolist())
for unique in ints_list:
ats.add_atoms(unique, 1)
for i in range(len(ats)):
ats.id[i] = i
#remove voronoi duplicates
print 'Fe_H atoms', len(ats)
ats.wrap()
del_ats = aseAtoms()
for at in ats:
del_ats.append(at)
geometry.get_duplicate_atoms(del_ats, cutoff=0.2, delete=True)
ats = del_ats.copy()
print 'Fe_H atoms remove duplicates', len(ats)
#select unique hydrogens
#for i in range(len(ats)):
# ats.id[i] = i
ints_list = [at.position for at in ats if at.number == 1]
with open('unique_h_sites.json', 'w') as f:
json.dump([list(u) for u in ints_list], f)
ats.write('hydrogenated_grain.xyz')
print 'Running WITH EAM as embedded cluster'
qm_pot_file = os.path.join(pot_dir, 'PotBH_fakemod.xml')
print qm_pot_file
mm_init_args = 'IP EAM_ErcolAd do_rescale_r=T r_scale=1.01' # Classical potential
qm_pot = Potential(mm_init_args, param_filename=qm_pot_file, cutoff_skin=cutoff_skin)
qmmm_pot = set_qmmm_pot(atoms, atoms.params['CrackPos'], mm_pot, qm_pot)
strain_atoms = fix_edges(atoms)
print 'Setup dynamics'
#If input_file is crack.xyz the cell has not been thermalized yet.
#Otherwise it will recover temperature from the previous run.
print 'Attaching trajectories to dynamics'
trajectory = AtomsWriter(traj_file)
#Only wriates trajectory if the system is in the LOTFDynamicas
#Interpolation
atoms.wrap()
atoms.set_cutoff(3.0)
atoms.calc_connect()
print 'Running Crack Simulation'
RELAXATION = False
if RELAXATION:
dynamics = FIRE(atoms)
dynamics.attach(pass_trajectory_context(trajectory, dynamics), traj_interval, dynamics)
dynamics.run(fmax=0.1)
else:
dynamics = LOTFDynamics(atoms, timestep, extrapolate_steps)
dynamics.attach(pass_trajectory_context(trajectory, dynamics), traj_interval, dynamics)
nsteps = 2000
dynamics.run(nsteps)